|
| Status |
Public on Jul 22, 2015 |
| Title |
cystic EBs d10 brB RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
cystic EBs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cystic EBs
developmental stage: 10 day differentiation
genetic background: C57Bl/6x129
es cell clone: Bl6/129 Jennifer Nichols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested with TriReagent using standard manufacturer protocol
(Sultan et al., 2012)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
processed data file format and content: *.F.bw are bigWig file for + strand mm10. *.R.bw are bigWig file for - strand mm10.
3 additional supplementary file on Series record: refSeqTranscriptsCountTable.txt (table of reads counts summarized over refSeq transcripts), refseqTranscriptsRPKMsTable.txt (table of RPKMs summarized over refSeq transcripts), and repeatMaskerIntergenicCountTable.txt (table of reads counts summarized over intergenic repeats (annotation from repeatmasker.org)).
RNAseq reads were aligned with GSNAP version 2012-12-12 alowing novel splicing events detection; ChIPseq reads were alined using GSNAP version 2012-12-12; WGBS reads were alined using GSNAP version 2012-12-12
read counts were summarized using RPKM_count.py from the RSeQC version 2.3.3 or using bedtools and further processed using custom scripts in R
peaks were called using MACS version 1.4.2 with the default settings
Whole genome bisulfite-seq metylation calling was done using bissnp pipeline
Genome_build: mm10
|
| |
|
| Submission date |
Mar 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Quanah J Hudson |
| E-mail(s) |
[email protected]
|
| Phone |
+43 1 4016070030
|
| Organization name |
CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14, AKH BT 25.3
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE56276 |
Imprinted expression is different in visceral yolk sac and cystic embryoid body endoderm |
|
| Relations |
| BioSample |
SAMN02709149 |
| SRA |
SRX501916 |
